| mm4550ThnL |
| ID: | 1509136318 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 394 (341) | ||
| Sequences: | 2173 (1462.6) | ||
| Seq/Len: | 6.372 | ||
| Nf(neff/√len): | 79.2 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 6.372).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 226_D | 230_S | 4.223 | 1.00 |
| 179_D | 208_R | 3.618 | 1.00 |
| 175_L | 208_R | 3.449 | 1.00 |
| 146_D | 180_A | 3.427 | 1.00 |
| 89_N | 144_D | 3.383 | 1.00 |
| 182_D | 211_E | 3.331 | 1.00 |
| 190_F | 214_L | 3.045 | 1.00 |
| 242_R | 279_E | 3.043 | 1.00 |
| 143_K | 147_R | 3.041 | 1.00 |
| 153_A | 184_A | 3.006 | 1.00 |
| 44_E | 141_L | 2.896 | 1.00 |
| 182_D | 208_R | 2.715 | 1.00 |
| 17_P | 39_W | 2.650 | 1.00 |
| 149_L | 180_A | 2.521 | 1.00 |
| 46_G | 121_A | 2.428 | 1.00 |
| 8_E | 11_R | 2.410 | 1.00 |
| 268_E | 329_D | 2.355 | 1.00 |
| 20_L | 37_A | 2.353 | 1.00 |
| 143_K | 151_E | 2.353 | 1.00 |
| 232_Y | 263_P | 2.289 | 1.00 |
| 87_A | 90_D | 2.288 | 1.00 |
| 10_R | 38_D | 2.256 | 1.00 |
| 203_P | 250_T | 2.244 | 1.00 |
| 171_P | 202_R | 2.231 | 1.00 |
| 225_T | 272_R | 2.219 | 1.00 |
| 203_P | 247_L | 2.218 | 1.00 |
| 271_A | 275_R | 2.187 | 1.00 |
| 119_F | 173_R | 2.173 | 1.00 |
| 119_F | 148_V | 2.132 | 1.00 |
| 259_F | 277_I | 2.081 | 1.00 |
| 175_L | 204_D | 2.063 | 1.00 |
| 190_F | 212_I | 2.023 | 1.00 |
| 179_D | 183_K | 2.021 | 1.00 |
| 150_A | 184_A | 2.006 | 1.00 |
| 326_P | 329_D | 1.975 | 1.00 |
| 207_A | 211_E | 1.959 | 1.00 |
| 129_F | 234_K | 1.954 | 1.00 |
| 178_A | 209_W | 1.946 | 1.00 |
| 39_W | 62_P | 1.909 | 1.00 |
| 315_D | 318_H | 1.905 | 1.00 |
| 218_L | 258_N | 1.889 | 1.00 |
| 207_A | 251_N | 1.880 | 1.00 |
| 180_A | 183_K | 1.818 | 1.00 |
| 219_V | 248_F | 1.813 | 1.00 |
| 270_F | 333_R | 1.777 | 1.00 |
| 222_E | 234_K | 1.765 | 1.00 |
| 7_R | 11_R | 1.753 | 1.00 |
| 146_D | 150_A | 1.714 | 1.00 |
| 240_Q | 243_R | 1.685 | 1.00 |
| 41_V | 52_L | 1.679 | 1.00 |
| 246_E | 250_T | 1.670 | 1.00 |
| 128_K | 301_E | 1.654 | 1.00 |
| 152_I | 181_I | 1.654 | 1.00 |
| 203_P | 251_N | 1.626 | 1.00 |
| 301_E | 305_Q | 1.602 | 1.00 |
| 152_I | 160_L | 1.580 | 0.99 |
| 93_M | 147_R | 1.574 | 0.99 |
| 51_R | 82_R | 1.555 | 0.99 |
| 257_A | 282_V | 1.550 | 0.99 |
| 192_M | 217_V | 1.539 | 0.99 |
| 21_G | 45_G | 1.533 | 0.99 |
| 242_R | 280_L | 1.490 | 0.99 |
| 180_A | 184_A | 1.474 | 0.99 |
| 6_S | 18_I | 1.470 | 0.99 |
| 243_R | 246_E | 1.451 | 0.99 |
| 206_I | 251_N | 1.449 | 0.99 |
| 249_H | 283_D | 1.440 | 0.99 |
| 7_R | 36_A | 1.435 | 0.99 |
| 233_R | 297_D | 1.423 | 0.99 |
| 148_V | 177_L | 1.411 | 0.99 |
| 271_A | 336_D | 1.385 | 0.98 |
| 206_I | 248_F | 1.377 | 0.98 |
| 153_A | 186_F | 1.372 | 0.98 |
| 51_R | 66_R | 1.366 | 0.98 |
| 44_E | 121_A | 1.365 | 0.98 |
| 167_A | 178_A | 1.360 | 0.98 |
| 214_L | 253_V | 1.358 | 0.98 |
| 121_A | 141_L | 1.358 | 0.98 |
| 95_D | 98_L | 1.341 | 0.98 |
| 302_S | 305_Q | 1.329 | 0.98 |
| 174_M | 178_A | 1.318 | 0.97 |
| 65_G | 68_L | 1.314 | 0.97 |
| 48_P | 82_R | 1.310 | 0.97 |
| 196_T | 219_V | 1.310 | 0.97 |
| 274_G | 337_L | 1.305 | 0.97 |
| 173_R | 177_L | 1.299 | 0.97 |
| 144_D | 147_R | 1.283 | 0.97 |
| 89_N | 147_R | 1.278 | 0.97 |
| 210_A | 253_V | 1.272 | 0.97 |
| 300_D | 304_D | 1.267 | 0.97 |
| 48_P | 67_G | 1.248 | 0.96 |
| 149_L | 153_A | 1.245 | 0.96 |
| 42_A | 69_A | 1.244 | 0.96 |
| 146_D | 176_E | 1.238 | 0.96 |
| 19_V | 49_L | 1.238 | 0.96 |
| 189_R | 215_D | 1.221 | 0.96 |
| 142_V | 173_R | 1.217 | 0.95 |
| 39_W | 52_L | 1.216 | 0.95 |
| 190_F | 209_W | 1.213 | 0.95 |
| 224_M | 273_L | 1.201 | 0.95 |
| 88_L | 92_P | 1.191 | 0.95 |
| 224_M | 276_T | 1.187 | 0.95 |
| 226_D | 238_A | 1.186 | 0.95 |
| 132_L | 165_D | 1.166 | 0.94 |
| 221_A | 241_T | 1.166 | 0.94 |
| 182_D | 212_I | 1.163 | 0.94 |
| 329_D | 332_H | 1.156 | 0.93 |
| 145_I | 177_L | 1.155 | 0.93 |
| 44_E | 88_L | 1.143 | 0.93 |
| 319_S | 331_Y | 1.142 | 0.93 |
| 174_M | 205_V | 1.141 | 0.93 |
| 3_R | 32_L | 1.134 | 0.93 |
| 150_A | 153_A | 1.132 | 0.93 |
| 247_L | 250_T | 1.124 | 0.92 |
| 117_I | 160_L | 1.121 | 0.92 |
| 177_L | 181_I | 1.117 | 0.92 |
| 8_E | 14_P | 1.116 | 0.92 |
| 25_P | 40_V | 1.110 | 0.92 |
| 24_H | 294_P | 1.109 | 0.92 |
| 167_A | 174_M | 1.106 | 0.91 |
| 10_R | 18_I | 1.103 | 0.91 |
| 175_L | 202_R | 1.099 | 0.91 |
| 210_A | 215_D | 1.096 | 0.91 |
| 24_H | 32_L | 1.096 | 0.91 |
| 19_V | 41_V | 1.093 | 0.91 |
| 13_W | 16_V | 1.091 | 0.91 |
| 145_I | 180_A | 1.078 | 0.90 |
| 258_N | 288_S | 1.076 | 0.90 |
| 262_Q | 266_V | 1.074 | 0.90 |
| 175_L | 179_D | 1.072 | 0.90 |
| 19_V | 39_W | 1.069 | 0.89 |
| 160_L | 188_K | 1.069 | 0.89 |
| 276_T | 280_L | 1.068 | 0.89 |
| 145_I | 149_L | 1.067 | 0.89 |
| 310_D | 313_L | 1.065 | 0.89 |
| 2_S | 20_L | 1.057 | 0.89 |
| 232_Y | 265_W | 1.053 | 0.88 |
| 9_A | 18_I | 1.051 | 0.88 |
| 275_R | 278_E | 1.046 | 0.88 |
| 41_V | 45_G | 1.041 | 0.88 |
| 269_D | 272_R | 1.034 | 0.87 |
| 128_K | 233_R | 1.029 | 0.87 |
| 229_L | 238_A | 1.028 | 0.87 |
| 246_E | 249_H | 1.028 | 0.87 |
| 6_S | 20_L | 1.022 | 0.86 |
| 266_V | 273_L | 1.021 | 0.86 |
| 129_F | 222_E | 1.020 | 0.86 |
| 24_H | 311_P | 1.016 | 0.86 |
| 10_R | 16_V | 1.016 | 0.86 |
| 148_V | 173_R | 1.015 | 0.86 |
| 120_T | 173_R | 1.015 | 0.86 |
| 10_R | 37_A | 1.015 | 0.86 |
| 39_W | 56_L | 1.011 | 0.86 |
| 168_F | 194_I | 1.010 | 0.85 |
| 261_V | 337_L | 1.008 | 0.85 |
| 228_E | 266_V | 1.001 | 0.85 |
| 247_L | 251_N | 1.001 | 0.85 |
| 41_V | 48_P | 1.000 | 0.85 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4jc0A | 2 | 0.835 | 100 | 0.626 | Contact Map |
| 2qgqA | 8 | 0.6015 | 100 | 0.732 | Contact Map |
| 4fhdA | 1 | 0.7132 | 99.9 | 0.738 | Contact Map |
| 1oltA | 1 | 0.7766 | 99.9 | 0.756 | Contact Map |
| 4wcxA | 2 | 0.8503 | 99.9 | 0.767 | Contact Map |
| 1r30A | 2 | 0.7081 | 99.9 | 0.771 | Contact Map |
| 3iixA | 1 | 0.7614 | 99.9 | 0.772 | Contact Map |
| 4rtbA | 1 | 0.8528 | 99.9 | 0.775 | Contact Map |
| 4u0oB | 1 | 0.6472 | 99.9 | 0.777 | Contact Map |
| 3t7vA | 1 | 0.7589 | 99.9 | 0.78 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)